I recently read a lesson, I think it was written by SilentDeftone about what chords are in what key, etc. Good lesson, but it left me wondering when I can use extended chords, and with which chords (whilst remaining in key).

For example; can I have a progression consisting mostly of open chords, and just throw in an obscure, complicated, extended chord whenever I want. Or can I only use extended/altered chords when they are ALL extended.

Sorry if I didn't explain that clear enough.

you can mix and match extended and simple chords to create whatever sound YOU want to hear...
if you mean what chords to play while remaining in key-depends on the additional notes added-but since things like Jazz Fusion many things may sound good and be out of key.